One of the most widely studied branches of biologically induced mineralization (BIM) processes is called microbially induced calcium carbonate precipitation (MICCP) also known as microbially induced calcite precipitation (MICP) can be used as a method for the reinterpretation of waste natural stone particles into a sustainable material. By overcoming the need for synthetic adhesives or energy consuming firing or sintering procedures for regaining such wastes, a natural and sustainable solution is proposed through certain biological treatment processes. The aim of this study was to determine main processing variables affecting the microbially induced biocement production using waste stone as a scaffold material. Bacillus pasteurii bacteria are used for biological induction of calcite precipitation. A custom-made reactor was designed for controlled incubation and media injection to the waste stone scaffold. Parameters examined were particle size of the waste stones, effect of stone type on cementation, urease activity of the bacterial culture, temperature, pH and flow rate of media, mechanical strength of cemented scaffolds and water absorption capacity. This research demonstrates a potential solution towards the waste generation problem of the global natural stone industry through the treatment of such wastes with biologically induced mineralization for creating a sustainable and biogenic material.